A B C D E F G H I J K L M N O P Q R S T U V W

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cacheInputFiles(Collection<File>) - Method in class biolockj.module.BioModuleImpl

Cache the input files for quick access on subsequent calls to BioModuleImpl.getInputFiles()

checkDependencies() - Method in interface biolockj.module.BioModule

During pipeline initialization, all configured BioModules will run this method to validate dependencies.

checkDependencies() - Method in class biolockj.module.BioModuleImpl

If restarting or running a direct pipeline execute the cleanup for completed modules.

checkDependencies() - Method in class biolockj.module.classifier.ClassifierModuleImpl

Validate module dependencies: Call ClassifierModuleImpl.getClassifierExe() to verify the executable Call ClassifierModuleImpl.getClassifierParams() to verify the runtime parameters are valid Call ClassifierModuleImpl.validateModuleOrder() to validate module configuration order.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.

checkDependencies() - Method in class biolockj.module.classifier.r16s.RdpClassifier

checkDependencies() - Method in class biolockj.module.classifier.wgs.Humann2Classifier

Verify that none of the derived command line parameters are included in Config."exe.humann2""Params".

checkDependencies() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier

Verify that none of the derived command line parameters are included in Config."exe.kraken2""Params".

checkDependencies() - Method in class biolockj.module.classifier.wgs.KrakenClassifier

Verify that none of the derived command line parameters are included in Config."exe.kraken""Params".

checkDependencies() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Verify none of the derived command line parameters are included in Config."exe.metaphlan2""Params"

checkDependencies() - Method in class biolockj.module.implicit.Demultiplexer

Validate module dependencies: If Config."demultiplexer.strategy" indicates use of barcodes to demultiplexer, validate metadata column named Config."metadata.barcodeColumn" exists Call Demultiplexer.setMultiplexedConfig() to set multiplexed Config if needed If Config."demultiplexer.barcodeCutoff" defined, validate between 0.0 - 1.0

checkDependencies() - Method in class biolockj.module.implicit.ImportMetadata

checkDependencies() - Method in class biolockj.module.implicit.parser.ParserModuleImpl

Execute ParserModuleImpl.validateModuleOrder() to validate module configuration order.

checkDependencies() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser

checkDependencies() - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables

Verify the previous module = QiimeClosedRefClassifier

checkDependencies() - Method in class biolockj.module.implicit.qiime.QiimeClassifier

checkDependencies() - Method in class biolockj.module.report.Email

Verify required email Config properties exist and are properly formatted.

checkDependencies() - Method in class biolockj.module.report.humann2.Humann2CountModule

checkDependencies() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts

checkDependencies() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts

checkDependencies() - Method in class biolockj.module.report.otu.RarefyOtuCounts

checkDependencies() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

checkDependencies() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

checkDependencies() - Method in class biolockj.module.report.r.R_CalculateStats

Validate configuration file properties used to build the R report: super.checkDependencies() Require "r_CalculateStats.pAdjustScope" Require "r_CalculateStats.pAdjustMethod"

checkDependencies() - Method in class biolockj.module.report.r.R_Module

checkDependencies() - Method in class biolockj.module.report.r.R_PlotEffectSize

At least one of the available plot types should NOT be disabled.

checkDependencies() - Method in class biolockj.module.report.r.R_PlotMds

Require Config."r_PlotMds.numAxis" set to integer greater than 2

checkDependencies() - Method in class biolockj.module.report.r.R_PlotOtus

checkDependencies() - Method in class biolockj.module.report.r.R_PlotPvalHistograms

checkDependencies() - Method in class biolockj.module.report.taxa.NormalizeTaxaTables

Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).

checkDependencies() - Method in class biolockj.module.ScriptModuleImpl

Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set

checkDependencies() - Method in class biolockj.module.seq.KneadData

checkDependencies() - Method in class biolockj.module.seq.Multiplexer

Validate module dependencies: Validate this is the last module to run (excluding Email) If this module was completed on a previous run, update the property: Config."internal.multiplexed" = "Y"

checkDependencies() - Method in class biolockj.module.seq.PearMergeReads

Validate module dependencies Verify input files are in fastq format Verify matching paired reads are found Validate required Config.PearMergeReads.EXE_PEAR property If running a restarted pipeline that already merged reads, set paired indicator to false

checkDependencies() - Method in class biolockj.module.seq.RarefySeqs

Validate module dependencies Validate Config.RarefySeqs.INPUT_RAREFYING_MIN is a non-negative integer Validate Config.RarefySeqs.INPUT_RAREFYING_MAX is a positive integer that is greater than or equal to Config.RarefySeqs.INPUT_RAREFYING_MIN (if defined)

checkDependencies() - Method in class biolockj.module.seq.TrimPrimers

Validates the file that defines the REGEX primers.

CLASS - Static variable in class biolockj.Constants

Config option for "report.taxonomyLevels": "class"

CLASS_DELIM - Static variable in class biolockj.node.OtuNodeImpl

Standard classifier output level delimiter for CLASS

ClassifierModule - Interface in biolockj.module.classifier

Classifier BioModules build one or more bash scripts to call the application on sequence files.

ClassifierModuleImpl - Class in biolockj.module.classifier

This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

ClassifierModuleImpl() - Constructor for class biolockj.module.classifier.ClassifierModuleImpl

classifyReportableMetadata(BioModule) - Static method in class biolockj.util.RMetaUtil

Classify and verify the R filter and reportable metadata fields listed in the Config file.
All metadata fields are reported unless specific fields are listed in: Config."r.reportFields".

cleanUp() - Method in interface biolockj.module.BioModule

This method executes after execution to update Config modified by the module or other cleanup operations.

cleanUp() - Method in class biolockj.module.BioModuleImpl

By default, no cleanUp code is required.

cleanUp() - Method in class biolockj.module.classifier.wgs.Humann2Classifier

cleanUp() - Method in class biolockj.module.implicit.Demultiplexer

Update SeqUtil to indicate data has been demultiplexed.

cleanUp() - Method in class biolockj.module.implicit.ImportMetadata

Verify the metadata fields configured for R reports.

cleanUp() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser

cleanUp() - Method in class biolockj.module.implicit.qiime.QiimeClassifier

The cleanUp operation builds a new metadata file if alpha diversity metrics were generated by this module.

cleanUp() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables

For R to report HumanN2 reports instead of taxa levels

cleanUp() - Method in class biolockj.module.report.otu.RarefyOtuCounts

Update ParserModuleImpl OTU_COUNT field name.

cleanUp() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

Update ParserModuleImpl OTU_COUNT field name.

cleanUp() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

Set the number of hits field.

cleanUp() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables

For R to report taxa levels (not HumanN2 reports)

cleanUp() - Method in class biolockj.module.seq.AwkFastaConverter

Set Config."internal.seqType" = "fasta"
Set Config."internal.seqHeaderChar" = SeqUtil.FASTA_HEADER_DEFAULT_DELIM

cleanUp() - Method in class biolockj.module.seq.PearMergeReads

Set Config."internal.pairedReads" = "N" and register number of reads.

cleanUp() - Method in class biolockj.module.seq.RarefySeqs

Set "Num_Rarefied_Reads" as the number of reads field.

cleanUp() - Method in class biolockj.module.seq.SeqFileValidator

Set "Num_Valid_Reads" as the number of reads field.

cleanUp() - Method in class biolockj.module.seq.TrimPrimers

Set "Num_Trimmed_Reads" as the number of reads field.

clearDemuxConfig() - Static method in class biolockj.util.DemuxUtil

Clear demultiplexer related fields

CLUSTER_BATCH_COMMAND - Static variable in class biolockj.util.BashScriptBuilder

Config String property: "cluster.batchCommand"
Terminal command used to submit jobs on the cluster.

CLUSTER_HOST - Static variable in class biolockj.module.report.Email

Config String property: "cluster.host"
The cluster host URL used for SSH and SCP connections.

CLUSTER_MODULES - Static variable in class biolockj.util.BashScriptBuilder

Config List property: "cluster.modules"
List of cluster modules to load at start of worker scripts.

CLUSTER_NUM_PROCESSORS - Static variable in class biolockj.util.BashScriptBuilder

One parameter of the Config String property "cluster.jobHeader" to set number of cores.

CLUSTER_PROLOGUE - Static variable in class biolockj.util.BashScriptBuilder

Config String property: "cluster.prologue"
To run at the start of every script after loading cluster modules (if any)

CLUSTER_VALIDATE_PARAMS - Static variable in class biolockj.util.BashScriptBuilder

Config Boolean property: "cluster.validateParams"
If set to "Y", validate "cluster.jobHeader" param cluster number of processors = "script.numThreads" or ScriptModule.SCRIPT_NUM_THREADS

COMBINED_FNA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Multiplexed fasta file produced by QIIME "add_qiime_labels.py" script: "combined_seqs.fna"

compareTo(BioModule) - Method in class biolockj.module.BioModuleImpl

compareTo(JsonNode) - Method in class biolockj.node.JsonNode

compareTo(OtuNode) - Method in class biolockj.node.OtuNodeImpl

The sort order of the TreeSet(OtuNode) is absolutely required for proper processing in OtuNodeImpl.addTaxa(String, String) and OtuNodeImpl.getTaxaMap().

compareTo(ParsedSample) - Method in class biolockj.node.ParsedSample

CompileOtuCounts - Class in biolockj.module.report.otu

This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.

CompileOtuCounts() - Constructor for class biolockj.module.report.otu.CompileOtuCounts

compileOtuCounts(Collection<File>) - Method in class biolockj.module.report.otu.CompileOtuCounts

Compile OTU counts from the individual sample OTU count files

compileSampleOtuCounts(File) - Static method in class biolockj.util.OtuUtil

Compile OTU counts from an individual sample OTU count file

COMPUTE_SCRIPT - Static variable in class biolockj.util.DockerUtil

Docker environment variable holding the name of the compute script file: "COMPUTE_SCRIPT"

Config - Class in biolockj

Provides type-safe, validated methods for storing/accessing system properties.
Initially populated by the properties in the Config file, several additional properties are created and stored in the the Config (to save system determined info such as: pipeline directory and name, has paired reads?, has multiplexed reads?, etc.).

Config() - Constructor for class biolockj.Config

CONFIG_DIR_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Config file directory path runtime parameter switch: "C"

CONFIG_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Config file path runtime parameter switch: "c"

ConfigException - Exception in biolockj.exception

ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.

ConfigException(String) - Constructor for exception biolockj.exception.ConfigException

Abstract Config exception calls super to instantiate using the superclass Exception implementation

ConfigException(String, String) - Constructor for exception biolockj.exception.ConfigException

Abstract Config exception calls ConfigException.buildMessage(String, String) to generate a standard error message for Configuration file errors, passing an empty string for the msg parameter.

ConfigFormatException - Exception in biolockj.exception

ConfigFormatException is thrown if property is defined but the format is invalid.

ConfigFormatException(String, String) - Constructor for exception biolockj.exception.ConfigFormatException

ConfigFormatException is thrown if property is defined but the format is invalid.

ConfigNotFoundException - Exception in biolockj.exception

ConfigNotFoundException is thrown if a required Config property is undefined.

ConfigNotFoundException(String) - Constructor for exception biolockj.exception.ConfigNotFoundException

ConfigNotFoundException is thrown if a required Config property is undefined.

ConfigPathException - Exception in biolockj.exception

ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.

ConfigPathException(File) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the filePath parameter does not exist on the file system.

ConfigPathException(File, String) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the filePath parameter does not exist on the file system.

ConfigPathException(String, String) - Constructor for exception biolockj.exception.ConfigPathException

ConfigPathException is thrown if the path does not exist or is not the proper file type: "file" or "directory".

ConfigViolationException - Exception in biolockj.exception

ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O (sequences or metadata) as defined by Config properties.

ConfigViolationException(String) - Constructor for exception biolockj.exception.ConfigViolationException

Generic exception message.

ConfigViolationException(String, String) - Constructor for exception biolockj.exception.ConfigViolationException

ConfigViolationException is thrown application detects a violation due to a Config property setting, such as finding Sample IDs with no corresponding sequence file enforced by Config."metadata.useEveryRow" = "Y"

Constants - Class in biolockj

Single Java class to hold shared constant values referenced my multiple classes.

Constants() - Constructor for class biolockj.Constants

CONTAINER_BLJ_DIR - Static variable in class biolockj.util.DockerUtil

Docker container BioLockJ installation directory: "/app/biolockj"

CONTAINER_BLJ_SUP_DIR - Static variable in class biolockj.util.DockerUtil

Docker container blj_support directory: "/app/blj_support"

CONTAINER_CONFIG_DIR - Static variable in class biolockj.util.DockerUtil

All containers mount the host Config directory to the container volume: "/mnt/efs/config"

CONTAINER_DB_DIR - Static variable in class biolockj.util.DockerUtil

Some containers mount a database to the containers "db" volume: "/mnt/efs/db"

CONTAINER_INPUT_DIR - Static variable in class biolockj.util.DockerUtil

All containers mount the host "input.dirPaths" to the container "input" volume: "/mnt/efs/input"

CONTAINER_META_DIR - Static variable in class biolockj.util.DockerUtil

Some containers mount the "metadata.filePath" to the container "meta" volume: "/mnt/efs/metadata"

CONTAINER_OUTPUT_DIR - Static variable in class biolockj.util.DockerUtil

All containers mount "internal.pipelineDir" to the container volume: "/mnt/efs/pipelines"

CONTAINER_PRIMER_DIR - Static variable in class biolockj.util.DockerUtil

Some containers mount the "trimPrimers.filePath" to the containers "primer": "/mnt/efs/primer" volume.

containsHn2ParserOutput(Collection<File>) - Static method in class biolockj.util.PathwayUtil

Check pipeline input contains Humann2Parser module output.

copyBatchOtuTableToOutputDir(File, Integer) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.

copyFileToPipelineRoot(File) - Static method in class biolockj.BioLockJ

Copy file to pipeline root directory.

copyInputData() - Static method in class biolockj.BioLockJ

Create a copy of the sequence files in property "input.dirPaths", output to a directory named "internal.pipelineDir"/input.

copyTempOtuTableToOutputDir() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.

countNumReads(File) - Static method in class biolockj.util.SeqUtil

Method counts number of reads in the given sequence file by counting the number of lines and dividing by the number of lines/sample (fasta=2, fastq=4)

createPipelineDirectory() - Static method in class biolockj.BioLockJ

Create the pipeline root directory under $DOCKER_PROJ and save the path to Config."internal.pipelineDir".

createScript(String, List<String>) - Static method in class biolockj.util.BashScriptBuilder

Create the script.

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